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- PDB-2lgi: Atomic Resolution Protein Structures using NMR Chemical Shift Tensors -

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Basic information

Entry
Database: PDB / ID: 2lgi
TitleAtomic Resolution Protein Structures using NMR Chemical Shift Tensors
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / GB1 / IMMUNOGLOBULIN BINDING DOMAIN / TEDOR / IGG-BINDING PROTEIN / PEPTIDOGLYCAN-ANCHOR / SECRETED / THERMOSTABLE
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodSOLID-STATE NMR / simulated annealing
Model detailsclosest to the average, model 10
AuthorsWylie, B.J. / Sperling, L.J. / Nieuwkoop, A.J. / Franks, W.T. / Oldfield, E. / Rienstra, C.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Ultrahigh resolution protein structures using NMR chemical shift tensors.
Authors: Wylie, B.J. / Sperling, L.J. / Nieuwkoop, A.J. / Franks, W.T. / Oldfield, E. / Rienstra, C.M.
History
DepositionJul 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2291
Polymers6,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6228.809 Da / Num. of mol.: 1 / Fragment: 2-1 repeat region residues 229-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06654

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D-NCA-{13C CST}
1213D-NCA-{1H-13C}
1313D-NCA-{13C CST}:{15N-13C}
1413D-NCA-1:1{13C CST}:{1H-13C}
1513D-NCA-2:1{13C CST}:{1H-13C}
1613D-NCA-3:1{13C CST}:{1H-13C}
1713D-NCA-{15N CST}
1813D-NCA-{1H-15N}
1913D-NCA-1:1{15N CST}:{1H-15N}
11013D-NCA-2:1{15N CST}:{1H-15N}
11113D-NCA-1:2{15N CST}:{1H-15N}

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Sample preparation

DetailsContents: 20 mg U-2-13C-glycerol; U-100% 15N GB1 / Solvent system: solid
SampleConc.: 20 mg/mL / Component: GB1-1 / Isotopic labeling: U-2-13C-glycerol; U-100% 15N
Sample conditionsIonic strength: 50 / pH: 5.5 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Varian Infinity Plus / Manufacturer: Varian / Model: Infinity Plus / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18.(2-4)Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.18.(2-4)Schwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
SpinEvolutionM.Veshtort, R.G.Griffindata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MinuitJames, F; Roos, Mdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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